The title is a reference to a Bible quotation, "O ye of little faith," from Matthew 6:30.
Bart's chalkboard gag was probably a subtle reference to his limited-edition breakfast cereal released in 2001, Bart Simpson Peanut Butter Chocolate Crunch Cereal by Kellogg's.
The model rocket attempted launches were partially based on the film October Sky.
When Ned joins Homer with his own model rocket, he greets him by saying, "Greetings from Nednedy Space Center on Cape Flandaveral," referencing the Kennedy Space Center and Cape Canaveral.
The large Jesus neon sign outside the church resembles the well-known neon "Vegas Vic" cowboy sign that was once atop the Pioneer Club in Las Vegas.
While walking into the new church, a man claims that he can exchange money for the patrons. Lisa remarks that it "could not be more blasphemous!" This is a reference to the biblical account of Jesus and the money changers.
There is a sign for the Zip Boys in the church, a parody of the Pep Boys.
On the Jumbo-tron, Lisa is captioned with the words "Pouting Thomas," a play on the phrase Doubting Thomas. The Jumbo-tron itself is labeled "Godcam."
This is also a reference to the 1970s episodes of Saturday Night Live where, after a sketch ended and before the show went to a commercial break, the camera would zoom in on someone in the audience and a bizarre or risque caption would appear below the shot.
When Reverend Lovejoy is done with his sermon, he introduces the Noid, the mascot of Domino's Pizza, to deliver a special sermon on the sanctity of deliciousness.
When Lovejoy says that the church has the same basic message, they just dressed it up a little, Lisa compares it to the Whore of Babylon.
When Bart proposes to Lisa to convert to Judaism, because "When you turn thirteen, cha-ching!" it is a reference to the Jewish Bar Mitzvah ceremony (which is valid only for males).
When Lenny refers to Richard Gere as the "world's most famous Buddhist," Gere asks, "What about the Dalai Lama?"
Carl asks Richard Gere if he really did all the sit-ups in An Officer and a Gentleman. Gere says that he only did one and they showed it a thousand times.
When Ned hears Lisa announce that she is a Buddhist, he exclaims, "My Satan sense is tingling!" This is a spoof of Spider-Man's catchphrase, "My Spidey-Sense is tingling!"
After the model rocket countdown, Homer shouts "countdown" rather than "ignition" or "blastoff."
The Rich Texan can be seen in the church, sitting in what would appear to be a skybox.
Marge tells Lisa she hopes at least one of the Simpsons will go to Heaven. In "Simpsons Bible Stories" that's what happened - Lisa starts ascending to Heaven, but Homer grabs her and takes her down to the barbecue in Hell along with the rest of the family.
When Marge tells Homer that this is the worst thing he's ever done, Homer replies that she's said it so much that the words have lost all meaning. Marge has also told Homer something is the worst thing he's ever done in "Brawl in the Family" (when it's revealed that Homer married the barmaid from Vegas). She's also said something very similar to that in "The Cartridge Family" (when Bart finds Homer's gun and uses it to play William Tell with Milhouse).
Syndication cuts a scene where as Homer's rocket is launched, a homeless person lying in the gutter, upon seeing the rocket, stops drinking his bottle of wine and throws it aside. A business man walking by at the time catches the bottle and immediately lies down in the gutter and starts drinking it.
This episode reveals that Homer wears contact lenses.